Match ups...how much weight to put on them

One dilemma that fantasy owners face from week to week is who to start. Later in the season, it gets easier as some players get hurt or are on bye. You also have many players step up to the 'must start' status. The tricky part comes when you have an average player with a great match up. Do you start them ahead of a top FFL player?
Normally, I play match up with running backs, but no other positions. Some teams are definitely susceptible to the run each year, so it's wise to start a rb against these teams (Philly this year). I also like to start rb's on teams I feel will win their game and shy away from those that will lose for obvious reasons. You don't always have the flexibility to play match ups, but when you do, it's a nice luxury.
My preference is to start your best players, unless your top player has a bad match up and your mediocre player has a good match up. I ran into this in one league last week and luckily it paid off. My first 2 picks in this league were Chris Johnson and Maurice Jones-Drew. Both sat on my bench last week. Instead I went with the favorable match ups of Fred Jackson (Oak) and James Starks (Car). Lucky for me, it worked, as Jackson (28) and Starks (11.5) both outscored my top rb's (CJ -6.5 MJD -10.7). However, my 2 top rb's will be back in the lineup this week as they have more favorable match ups.
It's very easy to over-think your weekly lineup. My advice is to play your top players every week and play match ups with your other starting spots. On the rare occasion that your top rb/qb is going up against a defense like Pittsburgh and your have an alternate option that has a favorable match up, you can bench a top tier player in favor of a 2nd or 3rd tier guy. I wouldn't make a habit out of benching your top picks, but sometimes it's warranted.